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Co-expression network analysis for identification of novel biomarkers of bronchopulmonary dysplasia model

BACKGROUND: Bronchopulmonary dysplasia (BPD) is the most common neonatal chronic lung disease. However, its exact molecular pathogenesis is not understood. We aimed to identify relevant gene modules that may play crucial roles in the occurrence and development of BPD by weighted gene co-expression n...

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Autores principales: Yu, Xuefei, Liu, Ziyun, Pan, Yuqing, Cui, Xuewei, Zhao, Xinyi, Li, Danni, Xue, Xindong, Fu, Jianhua
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9696732/
https://www.ncbi.nlm.nih.gov/pubmed/36440350
http://dx.doi.org/10.3389/fped.2022.946747
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author Yu, Xuefei
Liu, Ziyun
Pan, Yuqing
Cui, Xuewei
Zhao, Xinyi
Li, Danni
Xue, Xindong
Fu, Jianhua
author_facet Yu, Xuefei
Liu, Ziyun
Pan, Yuqing
Cui, Xuewei
Zhao, Xinyi
Li, Danni
Xue, Xindong
Fu, Jianhua
author_sort Yu, Xuefei
collection PubMed
description BACKGROUND: Bronchopulmonary dysplasia (BPD) is the most common neonatal chronic lung disease. However, its exact molecular pathogenesis is not understood. We aimed to identify relevant gene modules that may play crucial roles in the occurrence and development of BPD by weighted gene co-expression network analysis (WGCNA). METHODS: We used RNA-Seq data of BPD and healthy control rats from our previous studies, wherein data from 30 samples was collected at days 1, 3, 7, 10, and 14. Data for preprocessing analysis included 17,613 differentially expressed genes (DEGs) with false discovery rate <0.05. RESULTS: We grouped the highly correlated genes into 13 modules, and constructed a network of mRNA gene associations, including the 150 most associated mRNA genes in each module. Lgals8, Srpra, Prtfdc1, and Thap11 were identified as the key hub genes. Enrichment analyses revealed Golgi vesicle transport, coated vesicle, actin-dependent ATPase activity and endoplasmic reticulum pathways associated with these genes involved in the pathological process of BPD in module. CONCLUSIONS: This is a study to analyze data obtained from BPD animal model at different time-points using WGCNA, to elucidate BPD-related susceptibility modules and disease-related genes.
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spelling pubmed-96967322022-11-26 Co-expression network analysis for identification of novel biomarkers of bronchopulmonary dysplasia model Yu, Xuefei Liu, Ziyun Pan, Yuqing Cui, Xuewei Zhao, Xinyi Li, Danni Xue, Xindong Fu, Jianhua Front Pediatr Pediatrics BACKGROUND: Bronchopulmonary dysplasia (BPD) is the most common neonatal chronic lung disease. However, its exact molecular pathogenesis is not understood. We aimed to identify relevant gene modules that may play crucial roles in the occurrence and development of BPD by weighted gene co-expression network analysis (WGCNA). METHODS: We used RNA-Seq data of BPD and healthy control rats from our previous studies, wherein data from 30 samples was collected at days 1, 3, 7, 10, and 14. Data for preprocessing analysis included 17,613 differentially expressed genes (DEGs) with false discovery rate <0.05. RESULTS: We grouped the highly correlated genes into 13 modules, and constructed a network of mRNA gene associations, including the 150 most associated mRNA genes in each module. Lgals8, Srpra, Prtfdc1, and Thap11 were identified as the key hub genes. Enrichment analyses revealed Golgi vesicle transport, coated vesicle, actin-dependent ATPase activity and endoplasmic reticulum pathways associated with these genes involved in the pathological process of BPD in module. CONCLUSIONS: This is a study to analyze data obtained from BPD animal model at different time-points using WGCNA, to elucidate BPD-related susceptibility modules and disease-related genes. Frontiers Media S.A. 2022-11-07 /pmc/articles/PMC9696732/ /pubmed/36440350 http://dx.doi.org/10.3389/fped.2022.946747 Text en © 2022 Yu, Liu, Pan, Cui, Zhao, Li, Xue and Fu. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY) (https://creativecommons.org/licenses/by/4.0/) . The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Pediatrics
Yu, Xuefei
Liu, Ziyun
Pan, Yuqing
Cui, Xuewei
Zhao, Xinyi
Li, Danni
Xue, Xindong
Fu, Jianhua
Co-expression network analysis for identification of novel biomarkers of bronchopulmonary dysplasia model
title Co-expression network analysis for identification of novel biomarkers of bronchopulmonary dysplasia model
title_full Co-expression network analysis for identification of novel biomarkers of bronchopulmonary dysplasia model
title_fullStr Co-expression network analysis for identification of novel biomarkers of bronchopulmonary dysplasia model
title_full_unstemmed Co-expression network analysis for identification of novel biomarkers of bronchopulmonary dysplasia model
title_short Co-expression network analysis for identification of novel biomarkers of bronchopulmonary dysplasia model
title_sort co-expression network analysis for identification of novel biomarkers of bronchopulmonary dysplasia model
topic Pediatrics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9696732/
https://www.ncbi.nlm.nih.gov/pubmed/36440350
http://dx.doi.org/10.3389/fped.2022.946747
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